Source code setup

Installing from source code

3DMolMS can also be installed through source code:

git clone https://github.com/JosieHong/3DMolMS.git
cd 3DMolMS
pip install .

PyTorch must be installed separately. Check the official PyTorch website for the proper version for your system. For example:

pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu124

Update package locally

Every time you update the code, you can run the following command to update the package:

cd 3DMolMS
pip install .

Then you can use the package for various tasks as shown in the Source code usage and Advanced features page.

Requirements

3DMolMS has the following dependencies:

  • Python 3.8+

  • PyTorch

  • RDKit

  • NumPy

  • Pandas

  • matplotlib

  • PyYAML

  • Other dependencies listed in pyproject.toml

Most dependencies will be automatically installed when using pip, but PyTorch should be installed separately as mentioned above to ensure compatibility with your system’s CUDA version.